The sentence could be written either with the simple past tense or the present perfect. But the meaning would be different.
Simple past: "What estranged them from each other?" -- If we use the simple past, we don't know if they are still estranged or not. Maybe they later reconciled. Maybe not. We don't know.
Present perfect: "What has estranged them from each other?" -- Using the present perfect tense here relates the action to the present time. Therefore, we know that they are still estranged. The use of the present perfect often indicates that what happened in the past is still happening or is still in effect at the present time.